Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1274 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1218320197 sf1218291633 12 18320197 5.11E-09 2.72E-08
vg0225646452 sf0225640583 2 25646452 1.23E-08 6.51E-08
vg0425557776 sf0425372636 4 25557776 2.45E-08 1.78E-06
vg0707304077 sf0707303082 7 7304077 3.14E-08 1.51E-06
vg0808194223 sf0808193227 8 8194223 6.80E-08 2.80E-07
vg0124655774 sf0124654730 1 24655774 7.27E-08 2.20E-07
vg1222263107 sf1222229654 12 22263107 2.64E-07 9.85E-07
vg0200926863 sf0200926863 2 926863 2.87E-07 1.03E-06
vg1104497863 sf1104493765 11 4497863 4.40E-07 1.76E-06
vg0137912876 sf0137911833 1 37912876 5.49E-07 1.13E-06
vg1201180694 sf1201179694 12 1180694 5.69E-07 8.05E-07
vg0522137809 sf0522075251 5 22137809 6.04E-07 4.16E-07
vg1014510270 sf1014439036 10 14510270 9.98E-07 2.12E-06
vg0604320247 sf0604319248 6 4320247 1.27E-06 3.66E-06
vg1218539756 sf1218511192 12 18539756 NA 7.42E-06